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. 2024 Jun 21;21(9):1658–1667. doi: 10.1038/s41592-024-02316-4

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 10 — (a) Cross tabulation heatmap for the number of clusters between the RNA and protein data. (b) Modality weights from Seurat. (c) Within-modality weights of SpatialGlue explaining the contributions of the spatial and feature graphs to each cluster for each modality. (d) Spatial plots of data modalities with unimodal clustering (left), and clustering results (right) from single-cell and spatial multi-omics integration methods, Seurat, totalVI, MultiVI, MOFA+, MEFISTO, scMM, StabMap, and SpatialGlue. (e) Comparison of Moran’s I score. In the box plot, the center line denotes the median, box limits denote the upper and lower quartiles, and whiskers denote the 1.5× interquartile range. n = 5 clusters. (f) Comparison of Jaccard Similarity scores. (g) Between-modality weight explaining the importance of each modality to each cluster. (h) Within-modality weights explaining the contributions of the spatial and feature graphs to each cluster for each modality.